def __init__(self,
info_params,
allow_renames=True,
ignore_unused_sampled=False):
self.set_logger(lowercase=True)
self.allow_renames = allow_renames
# First, we load the parameters,
# not caring about whether they are understood by any likelihood.
# `input` contains the parameters (expected to be) understood by the likelihood,
# with its fixed value, its fixing function, or None if their value is given
# directly by the sampler.
self._infos = odict()
self._input = odict()
self._input_funcs = dict()
self._input_args = dict()
self._output = odict()
self._constant = odict()
self._sampled = odict()
self._sampled_renames = odict()
self._derived = odict()
self._derived_funcs = dict()
self._derived_args = dict()
# Notice here that expand_info_param *always* adds a _p_derived:True tag
# to infos without _prior or _p_value, and a _p_value field to fixed params
for p, info in info_params.items():
self._infos[p] = deepcopy(info)
if is_fixed_param(info):
if isinstance(info[_p_value], Number):
self._constant[p] = info[_p_value]
if not info.get(_p_drop, False):
self._input[p] = self._constant[p]
else:
self._input[p] = None
self._input_funcs[p] = get_external_function(
info[_p_value])
self._input_args[p] = getargspec(self._input_funcs[p]).args
if is_sampled_param(info):
self._sampled[p] = None
if not info.get(_p_drop, False):
self._input[p] = None
self._sampled_renames[p] = ((
lambda x: [x]
if isinstance(x, string_types) else x)(info.get(
_p_renames, [])))
if is_derived_param(info):
self._derived[p] = deepcopy(info)
# Dynamical parameters whose value we want to save
if info[_p_derived] is True and is_fixed_param(info):
info[_p_derived] = "lambda %s: %s" % (p, p)
if info[_p_derived] is True:
self._output[p] = None
else:
self._derived_funcs[p] = get_external_function(
info[_p_derived])
self._derived_args[p] = getargspec(
self._derived_funcs[p]).args
# Check that the sampled and derived params are all valid python variable names
for p in chain(self.sampled_params(), self.derived_params()):
if not is_valid_variable_name(p):
is_in = p in self.sampled_params()
eg_in = " p_prime:\n prior: ...\n %s: 'lambda p_prime: p_prime'\n" % p
eg_out = " p_prime: 'lambda %s: %s'\n" % (p, p)
raise LoggedError(
self.log,
"Parameter name '%s' is not a valid Python variable name "
"(it needs to start with a letter or '_').\n"
"If this is an %s parameter of a likelihood or theory, "
"whose name you cannot change,%s define an associated "
"%s one with a valid name 'p_prime' as: \n\n%s", p,
"input" if is_in else "output",
"" if is_in else " remove it and",
"sampled" if is_in else "derived",
eg_in if is_in else eg_out)
# Assume that the *un*known function arguments are likelihood output parameters
args = (set(chain(*self._input_args.values())).union(
chain(*self._derived_args.values())))
for p in (list(self._constant) + list(self._input) +
list(self._sampled) + list(self._derived)):
if p in args:
args.remove(p)
self._output.update({p: None for p in args})
# Useful sets: directly-sampled input parameters and directly "output-ed" derived
self._directly_sampled = [p for p in self._input if p in self._sampled]
self._directly_output = [p for p in self._derived if p in self._output]
# Useful mapping: input params that vary if each sampled is varied
self._sampled_input_dependence = odict(
[[s, [i for i in self._input if s in self._input_args.get(i, {})]]
for s in self._sampled])
# From here on, some error control.
dropped_but_never_used = (set([
p for p, v in self._sampled_input_dependence.items() if not v
]).difference(set(self._directly_sampled)))
if dropped_but_never_used and not ignore_unused_sampled:
raise LoggedError(
self.log,
"Parameters %r are sampled but not passed to the likelihood or theory "
"code, neither ever used as arguments for any parameters. "
"Check that you are not using the '%s' tag unintentionally.",
list(dropped_but_never_used), _p_drop)
# input params depend on input and sampled only, never on output/derived
all_input_arguments = set(chain(*self._input_args.values()))
bad_input_dependencies = all_input_arguments.difference(
set(self.input_params()).union(set(self.sampled_params())).union(
set(self.constant_params())))
if bad_input_dependencies:
raise LoggedError(
self.log,
"Input parameters defined as functions can only depend on other "
"input parameters that are not defined as functions. "
"In particular, an input parameter cannot depend on %r",
list(bad_input_dependencies))
def __init__(self,
info_params: Union[ParamsDict, ExpandedParamsDict],
allow_renames=True,
ignore_unused_sampled=False):
self.set_logger()
self.allow_renames = allow_renames
# First, we load the parameters,
# not caring about whether they are understood by any likelihood.
# `input` contains the parameters (expected to be) understood by the likelihood,
# with its fixed value, its fixing function, or None if their value is given
# directly by the sampler.
self._infos = {}
self._input: ParamValuesDict = {}
self._input_funcs = {}
self._input_args = {}
self._input_dependencies: Dict[str, Set[str]] = {}
self._dropped: Set[str] = set()
self._output: ParamValuesDict = {}
self._constant: ParamValuesDict = {}
self._sampled: ParamValuesDict = {}
self._sampled_renames: Dict[str, List[str]] = {}
self._derived: ParamValuesDict = {}
self._derived_inputs = []
self._derived_funcs = {}
self._derived_args = {}
self._derived_dependencies: Dict[str, Set[str]] = {}
# Notice here that expand_info_param *always* adds a "derived":True tag
# to infos without "prior" or "value", and a "value" field
# to fixed params
for p, info in info_params.items():
if isinstance(info, Mapping) and not set(info).issubset(partags):
raise LoggedError(self.log,
"Parameter '%s' has unknown options %s", p,
set(info).difference(partags))
info = expand_info_param(info)
self._infos[p] = info
if is_fixed_or_function_param(info):
if isinstance(info["value"], Real):
self._constant[p] = float(info["value"])
self._input[p] = self._constant[p]
if info.get("drop"):
self._dropped.add(p)
else:
self._input[p] = np.nan
self._input_funcs[p] = get_external_function(info["value"])
self._input_args[p] = getfullargspec(
self._input_funcs[p]).args
if is_sampled_param(info):
self._sampled[p] = np.nan
self._input[p] = np.nan
if info.get("drop"):
self._dropped.add(p)
self._sampled_renames[p] = str_to_list(
info.get("renames") or [])
if is_derived_param(info):
self._derived[p] = np.nan
# Dynamical parameters whose value we want to save
if info["derived"] is True and is_fixed_or_function_param(
info):
# parameters that are already known or computed by input funcs
self._derived_inputs.append(p)
elif info["derived"] is True:
self._output[p] = np.nan
else:
self._derived_funcs[p] = get_external_function(
info["derived"])
self._derived_args[p] = getfullargspec(
self._derived_funcs[p]).args
# Check that the sampled and derived params are all valid python variable names
for p in chain(self._sampled, self._derived):
if not is_valid_variable_name(p):
is_in = p in self._sampled
eg_in = " p_prime:\n prior: ...\n %s: " \
"'lambda p_prime: p_prime'\n" % p
eg_out = " p_prime: 'lambda %s: %s'\n" % (p, p)
raise LoggedError(
self.log,
"Parameter name '%s' is not a valid Python variable name "
"(it needs to start with a letter or '_').\n"
"If this is an %s parameter of a likelihood or theory, "
"whose name you cannot change,%s define an associated "
"%s one with a valid name 'p_prime' as: \n\n%s", p,
"input" if is_in else "output",
"" if is_in else " remove it and",
"sampled" if is_in else "derived",
eg_in if is_in else eg_out)
# input params depend on input and sampled only,
# never on output/derived unless constant
known_input = set(self._input)
all_input_arguments = set(chain(*self._input_args.values()))
bad_input_dependencies = all_input_arguments - known_input
if bad_input_dependencies:
raise LoggedError(
self.log,
"Input parameters defined as functions can only depend on other "
"input parameters. In particular, an input parameter cannot depend on %r."
" Use an explicit Theory calculator for more complex dependencies.\n"
"If you intended to define a derived output parameter use derived: "
"instead of value:", list(bad_input_dependencies))
# Assume that the *un*known function arguments are likelihood/theory
# output parameters
for arg in (all_input_arguments.union(*self._derived_args.values()).
difference(known_input).difference(self._derived)):
self._output[arg] = np.nan
# Useful set: directly "output-ed" derived
self._directly_output = [p for p in self._derived if p in self._output]
self._wrapped_input_funcs, self._wrapped_derived_funcs = \
self._get_wrapped_functions_evaluation_order()
# Useful mapping: input params that vary if each sample is varied
self._sampled_input_dependence = {
s: [
i for i in self._input
if s in self._input_dependencies.get(i, {})
]
for s in self._sampled
}
# From here on, some error control.
# Only actually raise error after checking if used by prior.
if not ignore_unused_sampled:
self._dropped_not_directly_used = self._dropped.intersection(
p for p, v in self._sampled_input_dependence.items() if not v)
else:
self._dropped_not_directly_used = set()
# warn if repeated labels
labels_inv_repeated = invert_dict(self.labels())
labels_inv_repeated = {
k: v
for k, v in labels_inv_repeated.items() if len(v) > 1
}
if labels_inv_repeated:
self.log.warning("There are repeated parameter labels: %r",
labels_inv_repeated)